Evaluates the best k-mer choice from programs choosing an optimal k in De Bruijn graphs. This evaluation pipeline uses snakemake, that requires python 3.x. Since most systems default to python2.X virtualenvs is the most convenient solution.
Install pyenv on uppmax (reccomended by UPPMAX as the default python virtual envirionment anyway) through the automatic installer pyenv-installer.
Then run
$ pyenv install 3.4.1
Now you have python 3.4.1 available through pyenv. Now install snakemake through pip3 or clone repository (see install_snakemake)
In the current shell, run
$ pyenv shell 3.4.1
to activate python 3 in the current shell. Now run,
$ snakemake
This will create output
To see a flowchart of the pipeline, run
$ snakemake --dag | dot -Tpdf > dag.pdf
Current detailed pipline:
Foe a compressed flowchart, run
$ snakemake --configfile config_local.json --rulegraph | dot -Tpng > figures/ruledag.png
Current detailed pipline:
